Thursday, February 28, 2013

Variations of the ‘cups and balls’ magic trick have been
performed for over two thousand years. One simple version involves three
inverted cups into which the performer loads brightly covered balls. Using sleight
of hand, the balls are moved in and out of the cups. Magicians hold many
beliefs about why this trick is so effective, one of which is that it’s
critical for the performer to mislead the audience with his direction of gaze.
Hector Rieiro, Susana Martinez-Conde and Stephen Macknik of the Barrow
Neurological Institute got the assistance of Teller (of the famed magical duo
‘Penn & Teller’) to test this. Even when Teller performs this trick with
clear cups he can still surprise an audience.

Seven subjects snuggled their chins onto mounts and watched
film clips of Teller performing different variations of cups and balls while
eye tracking devices monitored their gazes. They were asked to immediately
press one button as soon as a ball made physical contact with either a cup or
the table and a second button as soon as a ball stopped touching a cup or the
table. The volunteers consistently reported seeing the balls’ movements some
time after the actual movements. For example, people thought a ball was placed
in a cup after it had actually been placed there.

Interestingly, covering Teller’s face so that he couldn’t
use his own gaze to misdirect the viewers did not improve their performance.
This is contrary to most magicians’ intuition on the matter. Using gravity to
assist in the trick did not increase misdirection either, also a common magical
misconception.

Compare
two versions of the trick, a standard one, in which all three cups are treated the same way, and one in which Teller lifts up the third ball. More people were fooled by the latter. How about you?Rieiro, H., Martinez-Conde, S., & Macknik, S. (2013). Perceptual elements in Penn & Teller’s “Cups and Balls” magic trick PeerJ, 1 DOI: 10.7717/peerj.19.

Tuesday, February 26, 2013

There’s been some debate lately about
what to do about gun violence in the United States. A vast majority of citizens
on the left and the right are in favor of universal background checks (asking
about prior felonies and mental illness) for all gun purchasers. But would such
a measure be effective? According to a new study by Garen Wintemute of
the University of California, Davis, it would be.

Wintemute based his analysis on
currently existing laws and conditions. To begin with, he differentiates
between licensed dealers and private sellers. The former must collect
information from their customers before selling them weapons and then keep
permanent records on each sale. Private sellers have no such federal
requirement, although some states do require background checks for private
party sales. There is no limit as to how many guns a person can sell before
being legally considered a dealer rather than a private seller.

In many estimates, 40% of gun sales
do not involve licensed dealers and thus may not involve background checks.
That number increases to over 90% for ‘prohibited’ people who would not pass a
background check (presumably the sort of people we’d prefer to keep guns away
from) and to virtually 100% for juveniles seeking to buy weapons.

Wintemute then compared gun sales in
California, where even private sellers must do background checks on their
customers, and four states with no such restrictions (Arizona, Nevada, Texas
and Florida). In California gun shows, even private party sales are conducted
through licensed transfer agents. Sales in the other states can be, and usually
are, directly between seller and buyer. There were two consequences of this.
First, the gun shows across the California border in Nevada were full of
California buyers (over 30% by license plate count). Second, there were six
times as many illegal gun purchases (buying a gun for someone else who could
not pass a background check) in the neighboring states as in California.

These data strongly suggest that
federally mandated universal background checks and record keeping would prevent
many questionable people from purchasing firearms. People who could not pass a
check in California would not have the option of going to Nevada to get their
weaponry. This would be particularly helpful in cities like Chicago, which have
strict gun regulations but which get a huge influx of weapons from just outside
the city limits.

No one
is suggesting that universal background checks would solve all our problems.
They would however, undoubtedly reduce the number of guns available to people
who should not be trusted with guns, especially people with violent or unstable
histories. It’s no wonder that over 90% of Americans now favor enacting laws
requiring such measures.
For more details, watch Wintemute explain his findings below.

Update 4/2013: Mayors Against Illegal Guns has a fact sheet on background checks.

Monday, February 25, 2013

Although finding exoplanets is
interesting (and nearly a thousand have been confirmed to date), the really
exciting news would be to find another planet capable of sustaining life. To do
so, such a planet would almost certainly orbit within a certain radius from its
star: the ‘habitable zone’ (HZ). The trouble is, astronomers aren’t entirely
sure just what the boundaries of a star’s HZ are. Just recently, a team of
Pennsylvania State University cosmologists, led by Ravi Kopparapu, have
redefined the borders of the HZ.

The region within an HZ is largely determined by the presence of two
molecules: liquid water and carbon dioxide. If a planet is too close to its star, any water will boil off
into space. Too far, and the water will remain permanently frozen. Because the
outer edge of the HZ can be extended if the planet has a carbon dioxide
atmosphere to warm it, researchers take the presence of CO2 into
account when predicting the outermost limits of an HZ.

While Kopparapu and his colleagues
still use H20 and CO2 to define where an HZ will fall,
they believe that the criteria used to detect those molecules needs to be adjusted. When
they used updated data, they found that HZs tend to be a bit further out than
previously thought. This means that some planets that were written off may in
fact be within the HZ of their star, but also that some hopeful candidates
aren’t in the HZ after all.

Caption: The graphic shows
habitable zone distances around various types of stars. Some of the known
extrasolar planets that are considered to be in the habitable zone of their
stars are also shown. On this scale, Earth-Sun distance is one astronomical
unit, which is roughly 150 million kilometers.

Credit: Chester Herman

Notice that, according to the
new standards, Earth (seen near the top right) barely falls into the HZ of our sun. No doubt this new
model has some more tweaking in store.

Friday, February 22, 2013

We humans are well aware that our two eyes and ears gather
slightly different inputs that are combined into ‘stereo’ vision or hearing. We
also have two nostrils, close together as they are. Can we also smell in
stereo? If we’re like moles, we can.

Kenneth Catania of Vanderbilt
University used blind eastern American moles (Scalopus aquaticus) as his models. Although these moles have eyes, their
eyelids are fused shut, a reasonable adaptation for an animal that spends its
days swimming through dirt. Instead, the animal navigates its subterranean home
by using its nose.

Catania placed each mole in a
special testing chamber. Upon entering the chamber, the mole was presented with
a semicircle of 15 wells, only one of which contained a tasty tidbit (a segment
of earthworm). The moles were videotaped and monitored to detect sniffing
behavior. In some trials, one of the nostrils was blocked.

With both nostrils clear, the
moles were 100% accurate in bearing straight for the food-containing well.
However, with a nostril blocked, they first headed for one of the empty wells
70% of the time. More specifically, the moles were drifting toward the open
nostril. That is, when their left nostrils were blocked, they veered right and
vice versa. In all cases, the moles eventually found the food.

In a final set of experiments,
tubes were inserted into the moles nostrils such that airflow direction could
be switched. When these tubes were crossed, scent would flow into the left
nostril from the right side of the head and vice versa. This completely confused the moles and them to miss the food entirely. You can see some of these experiments below. Keep in
mind that these creatures are blind and are literally following their noses.

Taken together, these data
indicate that the moles are using their two nostrils to gather separate clues
about the location of their prey. If this were not the case, the moles should
have followed the same path toward the food regardless of whether they were
using one nostril or two (though perhaps a bit more slowly with only one
nostril). They aren’t merely getting less input with only one nostril, they’re
also losing directional information. This is no different than the change we
experience if one of our eyes or ears is blocked.

So does this finding apply to all mammals? That has yet to be seen,
though it’s certainly possible. Moles were a good model for this study because
their prey search isn’t confounded by visual clues as it would have been if Catania
had used dogs or rats. If humans have this ability we probably don’t notice it
as we rely so little on smell for orientation.Catania, K. (2013). Stereo and serial sniffing guide navigation to an odour source in a mammal Nature Communications, 4 DOI: 10.1038/ncomms2444.

Thursday, February 21, 2013

Because genetic engineering is so often misunderstood, I'd like to explain what it is. Genetic
engineering is simply a catch-all phrase for cultivation techniques that involve
direct manipulation of genes. You can add a gene to an organism that didn’t
previously have that gene or you can remove or alter an existing gene. Either
way, you’re limited to genetic changes that will be viable in the resulting
organism just as you would be by crossbreeding.

The following diagram compares
conventional breeding to genetic engineering (transgenesis or cisgenesis). By the way, a ‘cultivar’ is a
currently available version of the crop, and a ‘plasmid’ is a small circle of
DNA that functions as a vehicle for transferring your gene of interest. Note
that you have much less control over what gets added to the genome with conventional
breeding. Also, ‘many backcrosses’ could mean hundreds of generations.

This brings me to some important points. The fact that the genes have been manipulated doesn’t automatically make the result toxic. It depends on which genes have been added or altered. If you add beta-carotene genes to rice, you get a crop that could potentially save hundreds of thousands of children from dying or going blind from vitamin A deficiency. Sometimes, genetic engineering even brings unexpected benefits. For example, John Haegele and Frederick Below
from the University of Illinois found that Bt corn has much higher yields than conventional
corn. Bt corn is corn that is genetically engineered to contain a
gene from a soil bacterium named Bacillus thuringiensis (hence the ‘Bt’). The gene in question encodes a protein
that is toxic when ingested by a specific type of insect pest. It is not toxic
to other kinds of insects such as bees or beetles, and certainly not to humans
or other vertebrates. Bt corn does, however, have far less predation from
rootworms and consequently, the plants have a much healthier root system. This,
in turn, allows the plants to take up nitrogen more efficiently, resulting in higher
yields with less added fertilizer.

This is good news because
genetic engineering is here to stay. As more and more genomes are being
sequenced, it’s ridiculous to expect crop scientists to cross breed generation
after generation hoping to get a desired trait when they can just add the gene
they’re interested in. Perhaps more importantly, genetic engineering is
increasingly being used in medicine. It’s used to develop strains of mice or
other organisms that mimic human diseases, and to produce products such as
insulin and human growth hormone. Obviously, I’m
simplifying the work involved, but you get the idea. As a technique, genetic
engineering is far too useful to give up.Of course, there’s the possibility of purposefully or inadvertently adding harmful genes. But those are problems of misuse, not with the protocol itself. While there will undoubtedly be unanticipated problems, these problems can and should be managed responsibly. And just to be clear, ethical issues involving patents or business practices are not an indictment of the methodology behind genetic engineering.

Wednesday, February 20, 2013

On February 15th, a large meteor fell near the Russian city of Chelyabinsk, which is located just east of the Ural Mountains. Although spectacular, it did cause a fair amount of damage, including over a thousand injuries and many broken windows.

Here's a compilation video of the meteor including some of the aftermath:

More on this at Bad Astronomy and at The Guardian.Meanwhile, that same day another meteor was seen near San Francisco:Luckily, this one didn't cause any damage.Remember, this was also the same day that the asteroid 2012 DA14 did its close fly-by. Quite a day for sky-watchers.

Tuesday, February 19, 2013

Male silk moths are highly attuned to the odor of female
silk moths. When a male detects this odor, he begins a characteristic ‘dance’
designed to bring him into proximity with his paramour. During the first phase
of the dance, he walks in a straight line. You can get the moth to forego the
subsequent parts of the ritual (zig-zags and circles) by giving him another
whiff of pheromone. In that case, he’ll surge straight forward for each puff of
odor he detects. I think you can see where this is going. You can get a male
silk moth to follow a straight path by giving him a series of puffs of female silk
moth pheromone. Even better, you can get the moth to steer a robot for you.

Noriyasu Ando and his colleagues from the University of
Tokyo, attached a male adult silk worm to a free-floating polystyrene ball. You
can see the result below.

In both panels, puffs of pheromone directs the moth to steer
its track-ball controlled vehicle toward the source of the odor. In the
right-hand panel, the researchers have messed with the robot steering, making
it continuously veer to one side. In other experiments, the front of the tiny
car is covered, blinding the driver. Regardless of what the researchers threw
at it, the moth was able to steer toward the pheromone over 80% of the time.

I’m
pretty sure that the impetus for this research was not to help physically
handicapped silk moths find a partner. Rather, the scientists hope to adopt the insect’s odor tracking ability in driverless robots.

Monday, February 18, 2013

You may have heard of the bacteria
called Helicobacter pylori. They are
responsible for many of our gastric woes, such as ulcers and some types of
cancers. That being the case, you may think it’s a good thing that the microbes
are being eradicated in developed nations. Not so fast. H. pylori actually has a mixed record where human health is
concerned. Yes, it does cause ulcers, but on the other hand, there is some
evidence that H. pylori colonization
protects against asthma and allergies. Even more intriguingly, the bacteria may
also protect against obesity.

Electron micrograph of H. pylori possessing multiple flagellaH. pylori secrete chemicals that in turn affect the production of a variety of hormones manufactured by the gut epithelial cells. For example, when the
bacteria are present, ghrelin plasma levels go way down. Once H. pylori are eradicated, ghrelin levels rise.And what does ghrelin do? Stimulate the
appetite. H. pylori are also
associated with higher concentrations of the hormone leptin, which is
responsible for the feelings of satiety. So, is it a coincidence that developed
nations have both a low incidence of H. pylori infection and a high incidence of obesity? Josep Bassaganya-Riera of Virginia Tech and his colleagues
don’t think so.The researchers used a couple of
mouse models for their studies. One strain of mouse was deficient in leptin
receptors and the other were normal mice that were fed a high-fat diet. Either
way, the mice were expected to quickly become obese during the course of the
experiments. However, H. pylori infection had a number of effects on them.

Mice that were fed the high fat
diet had four times more leptin after being infected with H. pylori. Remember, this is a hormone that tells us it’s time to
stop eating. Fasting blood glucose levels were significantly lower in infected
mice of both types and returned to normal more quickly following a glucose
challenge. In addition, infected mice had less white adipose tissue, a.k.a.
fat. Finally, H. pylori carriers has
less insulin resistance than their uninfected cohorts. This suggests that H.
pylori may play a role in helping its
hosts maintain a healthy weight.

So, if you’ve been battling weight gain, should you have yourself
infected with H. pylori? That may not be the best idea
right now. First, there’s some chance you’re already a carrier. It’s estimated
that 80% of carriers are asymptomatic. Second, H. pylori
infection does have its downsides, not the least of which is an increased risk of duodenal and/or stomach cancer. However, it may one day be possible to
disassociate the pathogenic properties of H. pylori
from its metabolic effects. If that happens, we may all be getting dosed with H.
pylori.

At closest approach, occurring at
19:26 UTC (the updated time standard roughly synonymous with Greenwich Mean
Time), the asteroid will be about 17,000 miles from the surface of the Earth.
As you can see, that’s way inside the moon’s orbit, and even within the orbit
of satellites. Unfortunately, it’ll be too dim to see with the
naked eye.

Here’s more about it from the
folks at NASA.

You can learn lots more about it, including what would happen if it did hit us, from Phil Plait at Bad Astronomy.

Thursday, February 14, 2013

In order to successfully treat
cancer, it’s critical to identify the exact type of tumor afflicting the
patient. This is not only important for providing the correct treatment, but
also for avoiding wasting patients’ time with inappropriate treatments. Case in
point: triple negative breast cancer (TNBC).

Breast cancers are classified
in part by the type of receptors they express. TNBC tumors do not express any
of the three most common receptors: estrogen, progesterone or Her2. Not only do
TNBCs not respond to the types of treatment that non-TNBC tumors do, but there
are many TNBC subgroups that each require a different protocol. Clearly, the
sooner TNBCs can be identified and categorized, the better.

Kay Huebner from the Ohio
State University and her colleagues have found a way to distinguish TNBCs that
relies on the pattern of microRNAs (miRNAs) produced. These are tiny snippets
of RNA, no more than 25 nucleotides long, that affect gene expression by
binding to messenger RNA is specific places. Because TNBCs are, by definition,
deficient in receptor expression, the researchers thought that there could be
specific miRNAs targeting those gene sequences. This is exactly what they
found.

When the scientists compared
miRNAs in TNBC tumor cells versus non-tumor cells from the same women, there
were about a dozen of these nucleotide fragments that were altered. In some cases the tumor cells had more of the particular
miRNA, in others less of it.

The researchers also
determined the miRNA profile of metastatic tumors found in the lymph nodes of the same
women. Presumably, these tumors were derived from the original TNBC tumor
within the breast tissue. Nevertheless there were a few differences in the
miRNA profile between the lymph lesions and the TNBC or normal tissues. This
may lead to insights into the metastasis process.

Overall, the scientists were
able to develop two miRNA ‘signatures’ or patterns of upregulated and
downregulated miRNA. Patients with one combination of miRNAs had far better
long-term outcomes than those with the second, riskier pattern. The authors
suggest that doctors consider more aggressive therapies for such patients.

Wednesday, February 13, 2013

It's time again to see the winners of the Bioscapes
Competition sponsored by Olympus America. Prizes are given for the most
beautiful and/or extraordinary microscopic images, which can be either still or
videos. The winning entries must "depict subjects that are, or at one time
were, living". You can peruse the winners' gallery here.

Below
is the grand prize winner, an absolutely mesmerizing video of rotifers, taken
by Australian Ralph Grimm.

Tuesday, February 12, 2013

Proper protein folding is critical for cell functioning.
Lately, there’s been news that protein misfolding may be implicated in a range
of neurodegenerative diseases such as Parkinson’s, Huntington’s and
Alzheimer’s. Monte Willis and Cam Patterson of the University of North
Carolina, Chapel Hill, review the case that heart disease should be added to
the list.

There’s no doubt that the cardiomyocytes (heart cells) that
give the heart its contractile power live in a delicate balance of protein
formation and destruction. In a healthy heart, proteins are constantly being
turned over with new proteins being made and old or damaged proteins degraded
and removed from the cell. Misfolded proteins can be particularly problematic.

One problem is that misfolded proteins can assemble into
larger clumps that disrupt cell functions. And in fact, a variety of cardiac
stress disorders are associated with these protein masses. You can induce mouse
heart cells to accumulate aggregates of misfolded proteins by stressing them in
varying ways and you can observe these accumulations in the damaged hearts of
human patients.

These
and other lines of evidence suggest that protein folding is critical for proper
cardiac functioning. It also means that researchers would do well to focus on
preventing protein misfolding as a way to combat heart disease. One way to do this might be to increase the number of protein chaperones (quality control proteins that
ensure the proper folding and positioning of other proteins). Mice with a genetic predisposition to heart disease that had been given drugs
to increase the expression of these chaperones had significantly less cardiac disease
than their untreated fellows.

Monday, February 11, 2013

The Federal Drug
Administration (FDA) has strict guidelines about recruiting participants in
medical studies. Subjects must be able to fully consent to the procedures being
evaluated. This is all well and good, but what about procedures specifically
geared to helping people who have suffered some life-threatening trauma? Such
individuals are often in no condition to consent even if doctors had the time
to wait for such approval before acting. Yet, without clinical trials, it’s
difficult for medical professionals to learn and improve their treatment
methods.

Because of this, in 1996, the
FDA established an Exception from Informed Consent (EFIC) policy. If an
incapacitated patient meets specific criteria (his condition is immediately life-threatening
and may benefit from the proposed treatment), doctors can enroll him in a
clinical trial without his or his family’s consent. Carrie Sims of the
University of Pennsylvania and her colleagues wondered what people think about
this.

The researchers queried 172
trauma patients and their family members just prior to discharge from a
hospital about their attitudes concerning the EFIC policy. In particular, the
subjects were asked whether they would have been willing to participate in
trials using a blood substitute if they had suffered extreme blood loss. Well
over 90% of participants, both patients and family members, agreed that general
research into handling trauma was critical. The same number thought that tests
of the specific blood products mentioned should be done. Two thirds of people
thought it would have been acceptable to enroll a family member in such studies
without anyone having given consent. That number increased to three quarters
for enrolling themselves.

Clearly,
people see a need for clinical research and understand that such research is
especially important for treating people who are on the verge of death. On the
other hand, informed consent guidelines exist for a reason, not least to
prevent unethical experimentation on vulnerable people. The EIFC policy may be
a way to achieve the goal of testing emergency procedures while still adhering
to specific codes of conduct.

Friday, February 8, 2013

To be clear, we’re not talking about storing DNA itself. DNA is actually
surprisingly stable and, under the right conditions, can last thousands of
years without degrading. No, the idea is to use DNA as a medium for storing
other kinds of information. For example, Nick Goldman and his colleagues from
the European Bioinformatics Institute have used DNA to store all of
Shakespeare’s sonnets, a color photograph and a sound recording of Martin
Luther King Junior. The authors believe that their new technique could one day
solve all our data archiving needs in perpetuity.

The idea of using DNA to store information is not new. DNA
has long been thought an attractive data depository because all it requires for
long-term maintenance is a cool, dark environment. You can also fit an amazing
amount of data in a small space. The authors estimate that all the data that’s
ever been created could fit in the back of one pick-up truck. And best
of all, because the nucleotides don’t change, unlike cassette tapes and DVDs, the same decoding technology
should work a thousand years from now.

To use DNA for data storage, you simply manufacture DNA
using the sequence of As, Ts, Gs and Cs as a code to spell out whatever you
wish. To be clear, these synthetic strands of DNA will not encode any genes.
That is, like magnetic tape or ink, they will not have any function other than
to store or retrieve information. Unfortunately, at this time, it’s exceedingly difficult to
synthesize DNA that’s much longer than a hundred bases long, barely enough for
a sentence. Almost any data file would have to be broken into a huge number of
pieces that would then have to be faithfully joined together. Goldman and his
colleagues improved upon this both by creating a novel code and by using
four-fold redundancy.

Briefly, the researchers took the information to be
DNA-itized (a sonnet in the example below) and converted it first into binary code (shown blue below) and then
into a novel trinary code (0s, 1s and 2s, shown in red) where each digit is represented by two
nucleotides. The resulting sequence of DNA (green) was synthesized in short overlapping
fragments, so that each data point was found in four distinct pieces. Each
fragment of DNA contained tags indicating where to fit it in order to
regenerate the original sequence. The high degree of redundancy ensured accurate
retrieval. Nature PMID: 23354052.The scientists were able to send their DNA from the U.S. to Germany,
where it was correctly reconstructed and decoded.

As of now, even this new method of DNA storage is far too
expensive and has too slow a retrieval rate to be of any practical use. The
authors have every expectation that this will change. Perhaps in as little as
ten years, DNA will be the medium of choice for our data storage needs.

Thursday, February 7, 2013

While almost everyone today is connected to other people via
the internet, some people make far greater use of these tools than
others. Luis Vaquero of Hewlett-Packard Laboratories,
Bristol and Manuel Cebrian of the University of California at San Diego and
NICTA, Melbourne were interested in how college students interact with one
another online and how this affects their success in school. To that end, they
studied how much students communicated with one another and under what
circumstances. I doubt you’ll be surprised to hear that the best students
formed the most complex social networks.

All in all, the researchers
followed 290 students through some 80,000 interactions. You can see a sample
classroom below.

The squares each represent one of the 82 students in the class, and the lines represent the interactions
between those students. The most persistent interactions are shown as thick
blue lines and more transient interactions as dotted grey lines. The highest
performing students are represented as dark blue, mid-performers as red and
low-performers as green squares.

As you can see, there is a
strong correlation between the number and persistence of interactions with
fellow students and success in the classroom. The highest performing students
formed the most persistent interactions with each other. While low-performing
students would initiate contact with mid or high-performers, those students
often did not reciprocate. In addition, although all students make some attempt
at contact with their cohorts during the first few weeks of each semester,
low-performing students quickly stopped interacting with their peers. In
contrast, the high and mid performers peek in interactions by week four and
maintain a high level of contact for the rest of the semester.

The
authors are quick to point out that the students were not trying to be exclusionary.
It’s just that the best students tend to identify one another rather quickly at
the beginning of each course and find that it’s to their mutual benefit to
maintain contact. Vaquero and Cebrian refer to this collaborative relationship
as a ‘rich-club’ and suggest that college students who want to do well try to
get into one. Vaquero, L., & Cebrian, M. (2013). The rich club phenomenon in the classroom Scientific Reports, 3 DOI: 10.1038/srep01174.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.